Mogliman

Vehicle is a 2000 Audi TT
Let me start off by saying I have run countless searches and researched this problem to no end. All the information online has been fantastic and I have trouble-shooted everything I can possibly think of based off of the information I have found online.
Initial Issue:
EPC light came on while driving on the highway and car went into limp mode.
Received the following engine codes.
P1542 Angle Sensor 1 (G187) Implausible signal.
P1171 Angle Sensor 2 (G188) Implausible signal.
I replaced the throttle body and has the same issues.
Thanks to all of the great advice online I was able to find that my O2 sensor before the Cat has melted and shorted out. This fried the ECM, and killed the circuit that controls the throttle body.
So a couple of days later I was finally able to get my hands onto a new ECU. I plugged this in with both O2 sensors unplugged.
Now I get
P1545 Throttle Valve controller Malfunction.
And 1 of
P1542 Angle Sensor 1 (G187) Implausible signal.
P1171 Angle Sensor 2 (G188) Implausible signal.
But never both.
Now to list the things I have done to troubleshoot further wiring problems.
I Have:
1. Verified wiring from TB connect to ECM. Some wires would show as open if the wire was wiggled around. This connector has now been re-pinned and no longer showing an issue.
2. Verified both O2 sensor connects are not shorted to ground or open from pins connected at ECM.
3. Verified all expected voltages from accelerator pedal, and throttle body and all seem to match exactly what the manual says.
4. Getting resistance values between 1.3-1.5 KΩ across both potentiometers on both throttle bodies.
5. Getting resistance values of 1.4Ω and 2.4Ω across the motor for the throttle bodies. (unsure if these readings are corrected or if I have two messed up throttle bodies.)
Currently when going to adapt the throttle body two out of 3 times it will fail and come up with ERROR. In the 1 in 3 times it does come back with ADP ok I still have the P1545 malfunction code. Some of the time this code too will clear and I will show no coded. When the adp ok shows if I go into Measuring block 62 I see accurate readings in all 4 cells and the throttle body itself does open and close. My accelerator pedal reading both go up and 1 is half of the other and my throttle body readings are inversely proportional.
All of this changes once I turn the key from just being on to start. As soon as the motor physically starts up the EPC light stays on. I will get code P1545 and (P1542 or P1171).
One this happens I can still see accurate readings for my accelerator pedal but the throttle body only moves a few percent if at all.
Please if any has any advice or suggestions please let me know. I am at my wits end and am now at a loss of what to check next.
Unsure if
BAD ECM
TWO Bad throttle bodies or some other misc. thing I cannot even fathom.

Thanks in advance